Survivors of sexual violence are at higher risk of adverse mental health outcomes compared to those exposed to other interpersonal traumas. To examine the trajectory of both post-traumatic stress disorder (PTSD) and depression as well as the role of early counselling over 24 months among rape survivors. The South African Rape Impact Cohort Evaluation (RICE) study enrolled women aged 16-40 years attending post-rape care services within 20 days of a rape incident ( = 734), and a comparison group ( = 786) was recruited from primary health care. Women were followed for 24 months; the main study outcomes were depression and PTSD. Reports of early supportive counselling by the exposed group were also included. The analysis included an adjusted joint mixed model with linear splines to account for correlated observations between the outcomes. At 24 months, 45.2% of the rape-exposed women met the cut-off for depression and 32.7% for PTSD. This was significantly higher than levels found among the unexposed. Although a decline in depression and PTSD was seen at 3 months among the women who reported a rape, mean scores remained stable thereafter. At 24 months mean depression scores remained above the depression cut-off (17.1) while mean PTSD scores declined below the PTSD cut-off (14.5). Early counselling was not associated with the trajectory of either depression or PTSD scores over the two years in rape-exposed women with both depression and PTSD persisting regardless of early counselling. The study findings highlight the importance to find and provide effective mental health interventions post-rape in South Africa.